suppressPackageStartupMessages({
library(tidyverse)
})
# Detect the ".git" folder -- this will be in the project root directory
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal")
results_dir <- file.path(analysis_dir, "results")
input_dir <- file.path(analysis_dir, "input")
files_dir <- file.path(root_dir, "analyses", "sample-distribution-analysis", "results")
# Input files for the paired longitudinal (PL) cohort
pbta_file <- file.path(files_dir, "pbta.tsv") # file from add-sample-distribution module
genomic_paired_file <- file.path(files_dir, "genomic_assays_matched_time_points.tsv")
tmb_vaf_file <- file.path(results_dir, "tmb_vaf_genomic.tsv")
palette_file <- file.path(root_dir, "figures", "palettes", "oncoprint_color_palette.tsv")
# Input files for the PBTA cohort
maf_file <- file.path(results_dir, "maf.tsv")
tmb_file <- file.path(input_dir, "snv-mutation-tmb-coding.tsv")
# File path to PL plot directory
PL_plots_dir <-
file.path(analysis_dir, "plots", "Alteration_type_barplots_PL")
if (!dir.exists(PL_plots_dir)) {
dir.create(PL_plots_dir)
}
# File path to kids_PL_plots directory
kids_PL_plots_dir <-
file.path(PL_plots_dir, "kids_PL_plots")
if (!dir.exists(kids_PL_plots_dir)) {
dir.create(kids_PL_plots_dir)
}
# File path to kids_molecular_subtype_PL_plots_dir directory
kids_molecular_subtype_PL_plots_dir <-
file.path(PL_plots_dir, "kids_molecular_subtype_PL_plots")
if (!dir.exists(kids_molecular_subtype_PL_plots_dir)) {
dir.create(kids_molecular_subtype_PL_plots_dir)
}
# File path to molecular_subtype_PL_plots directory
molecular_subtype_PL_plots_dir <-
file.path(PL_plots_dir, "molecular_subtype_PL_plots")
if (!dir.exists(molecular_subtype_PL_plots_dir)) {
dir.create(molecular_subtype_PL_plots_dir)
}
# File path to PBTA plot directory
PBTA_plots_dir <-
file.path(analysis_dir, "plots", "Alteration_type_barplots_PBTA")
if (!dir.exists(PBTA_plots_dir)) {
dir.create(PBTA_plots_dir)
}
# File path to molecular_subtype_PBTA_plots directory
molecular_subtype_PBTA_plots_dir <-
file.path(PBTA_plots_dir, "molecular_subtype_PBTA_plots")
if (!dir.exists(molecular_subtype_PBTA_plots_dir)) {
dir.create(molecular_subtype_PBTA_plots_dir)
}
source(paste0(root_dir, "/figures/scripts/theme.R"))
source(paste0(analysis_dir, "/util/function-create-barplot.R"))
# Vector to order timepoints
timepoints_order <- c("Diagnosis", "Progressive", "Recurrence", "Deceased", "Second Malignancy", "Unavailable", "Metastatic", "Residual")
timepoints_order_abbrev <- c("Dx", "Pro", "Rec", "Dec", "SM", "Unavail", "Metastatic", "Residual")
# Vector to order Variant_Classification
variants_order <- c("Frame_Shift_Del", "Frame_Shift_Ins", "In_Frame_Del",
"In_Frame_Ins", "Missense_Mutation", "Nonsense_Mutation",
"Nonstop_Mutation", "Splice_Site", "Translation_Start_Site")
pbta_df <- readr::read_tsv(pbta_file, guess_max = 100000, show_col_types = FALSE) %>%
select(Kids_First_Participant_ID, Kids_First_Biospecimen_ID, cg_multiple, cg_id, cgGFAC, tumor_descriptor, molecular_subtype) %>% #plot_group
mutate(tumor_descriptor_abbrev = case_when(grepl("Diagnosis", tumor_descriptor) ~ "Dx",
grepl("Progressive", tumor_descriptor) ~ "Pro",
grepl("Recurrence", tumor_descriptor) ~ "Rec",
grepl("Deceased", tumor_descriptor) ~ "Dec",
grepl("Second Malignancy", tumor_descriptor) ~ "SM",
grepl("Unavailable", tumor_descriptor) ~ "Unavail",
TRUE ~ tumor_descriptor),
molecular_subtype = str_replace(molecular_subtype, ",", ""),
molecular_subtype_edited = str_replace(molecular_subtype, "^\\S* ", ""),
# create unique identifier for timepoint and molecular subtype
td_ms_plot_group = paste(tumor_descriptor_abbrev, molecular_subtype_edited, sep = ":"))
# This includes non synonymous mutations as described in the `01-preporcess-data.Rmd`
tmb_vaf_df <- readr::read_tsv(tmb_vaf_file, guess_max = 100000, show_col_types = FALSE) %>%
filter(!tmb >= 10) %>%
select(Kids_First_Biospecimen_ID, Variant_Classification, gene_protein, mutation_count, region_size, tmb, VAF) %>%
filter(!is.na(Variant_Classification))
# List with patients with paired longitudinal genomic specimens
genomic_paired_df <- readr::read_tsv(genomic_paired_file, guess_max = 100000, show_col_types = FALSE) %>%
left_join(pbta_df, by = c("Kids_First_Participant_ID")) %>%
left_join(tmb_vaf_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!is.na(tmb))
# Number of patients with TMB information
no_samples_with_tmb <- print(length(unique(genomic_paired_df$Kids_First_Participant_ID)))
[1] 116
# Attention as some bs specimen might not have TMB.
# If that happens, we will end up with samples lacking timepoints.
# Let's identify these samples and remove them.
PL_df <- genomic_paired_df %>%
select(Kids_First_Participant_ID, tumor_descriptor) %>%
unique() %>%
arrange(Kids_First_Participant_ID, tumor_descriptor) %>%
group_by(Kids_First_Participant_ID) %>%
summarize(tumor_descriptor_sum = str_c(tumor_descriptor, collapse = ";")) %>%
filter(!tumor_descriptor_sum %in% c("Diagnosis", "Progressive", "Recurrence", "Second Malignancy", "Unavailable", "Deceased", "Progressive;Progressive")) %>%
left_join(genomic_paired_df, by = c("Kids_First_Participant_ID")) %>%
filter(!cg_id == "NA",
!tumor_descriptor == "Not Reported") %>%
mutate(match_id = paste(tumor_descriptor, Kids_First_Participant_ID, sep = "_"),
cg_id = str_replace(cg_id, c("/|-"), " "))
# Let's summarize td_ms_plot_group and use this for visualization purposes
PL_td_ms_plot_group_n_df <- PL_df %>%
dplyr::count(cg_id, td_ms_plot_group) %>%
dplyr::mutate(td_ms_plot_group_n = glue::glue("{td_ms_plot_group} (N={n})")) %>%
dplyr::rename(td_ms_plot_group_number = n)
# Let's summarize tumor_descriptor and use this for visualization purposes
PL_td_plot_group_n_df <- PL_df %>%
dplyr::count(cg_id, tumor_descriptor) %>%
dplyr::mutate(td_plot_group_n = glue::glue("{tumor_descriptor} (N={n})")) %>%
dplyr::rename(td_plot_group_number = n)
# Let's count number of samples
PL_count_df <- PL_df %>%
left_join(PL_td_ms_plot_group_n_df) %>%
left_join(PL_td_plot_group_n_df) %>%
filter(!is.na(Variant_Classification)) %>%
# remove if total #samples per timepoint is less than 2
#filter(!td_ms_plot_group_number <= 2) %>%
group_by(tumor_descriptor, td_ms_plot_group, cg_id, molecular_subtype, Kids_First_Participant_ID, match_id, Variant_Classification, td_ms_plot_group_n, td_plot_group_n) %>%
dplyr::count(Kids_First_Participant_ID) %>%
mutate(tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order),
Variant_Classification = factor(Variant_Classification),
Variant_Classification = fct_relevel(Variant_Classification, variants_order)) %>%
arrange(tumor_descriptor, Variant_Classification, desc(molecular_subtype))
Joining with `by = join_by(cg_id, td_ms_plot_group)`Joining with `by = join_by(cg_id, tumor_descriptor)`Warning: There were 945 warnings in `mutate()`.
The first warning was:
ℹ In argument: `tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order)`.
ℹ In group 1: `tumor_descriptor = "Deceased"`, `td_ms_plot_group = "Dec:ADAM"`, `cg_id = "Adamantinomatous Craniopharyngioma"`, `molecular_subtype =
"CRANIO ADAM"`, `Kids_First_Participant_ID = "PT_WYXTEG3E"`, `match_id = "Deceased_PT_WYXTEG3E"`, `Variant_Classification = "Frame_Shift_Del"`,
`td_ms_plot_group_n = "Dec:ADAM (N=21)"`, `td_plot_group_n = "Deceased (N=21)"`.
Caused by warning:
! 3 unknown levels in `f`: Unavailable, Metastatic, and Residual
ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 944 remaining warnings.
# Number of patients with TMB information and paired timepoints
no_samples <- print(length(unique(PL_count_df$Kids_First_Participant_ID)))
[1] 107
tmb_df <- readr::read_tsv(tmb_file, guess_max = 100000, show_col_types = FALSE) %>%
dplyr::rename(Kids_First_Biospecimen_ID = Tumor_Sample_Barcode) # change name of the biospecimen to match the one from the histologies files
tmb_vaf_df <- readr::read_tsv(maf_file, guess_max = 100000, show_col_types = FALSE) %>%
left_join(tmb_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!tmb >= 10,
!is.na(tmb))
PBTA_df <- pbta_df %>%
left_join(tmb_vaf_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!cg_id == "NA",
!tumor_descriptor == "Not Reported",
!is.na(Variant_Classification)) %>%
mutate(match_id = paste(tumor_descriptor, Kids_First_Participant_ID, sep = "_"),
cg_id = str_replace(cg_id, c("/|-"), " "))
# Number of patients with TMB information
no_samples <- print(length(unique(PBTA_df$Kids_First_Participant_ID)))
[1] 1850
# Let's summarize tumor_descriptor and use this for visualization purposes
PBTA_td_plot_group_n_df <- PBTA_df %>%
dplyr::count(cg_id, tumor_descriptor) %>%
dplyr::mutate(td_plot_group_n = glue::glue("{tumor_descriptor} (N={n})")) %>%
dplyr::rename(td_plot_group_number = n)
# Let's count number of samples
PBTA_count_df <- PBTA_df %>%
left_join(PBTA_td_plot_group_n_df, by = join_by("cg_id", "tumor_descriptor")) %>%
filter(!is.na(Variant_Classification)) %>%
group_by(tumor_descriptor, cg_id, molecular_subtype, Kids_First_Participant_ID, match_id, Variant_Classification, td_plot_group_n) %>%
dplyr::count(Kids_First_Participant_ID) %>%
mutate(tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order),
Variant_Classification = factor(Variant_Classification),
Variant_Classification = fct_relevel(Variant_Classification, variants_order)) %>%
arrange(tumor_descriptor, Variant_Classification, desc(molecular_subtype))
Warning: There were 6564 warnings in `mutate()`.
The first warning was:
ℹ In argument: `tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order)`.
ℹ In group 1: `tumor_descriptor = "Deceased"`, `cg_id = "Adamantinomatous Craniopharyngioma"`, `molecular_subtype = "CRANIO ADAM"`,
`Kids_First_Participant_ID = "PT_WYXTEG3E"`, `match_id = "Deceased_PT_WYXTEG3E"`, `Variant_Classification = "Frame_Shift_Del"`, `td_plot_group_n =
"Deceased (N=21)"`.
Caused by warning:
! 1 unknown level in `f`: Unavailable
ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 6563 remaining warnings.
# Read color palette
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE) %>%
mutate(hex_codes = case_when(grepl("#000000", hex_codes) ~ "orange",
TRUE ~ hex_codes),
color_names = factor(color_names),
color_names = fct_relevel(color_names, variants_order)) %>%
arrange(color_names)
# Define and order palette
palette <- palette_df$hex_codes
names(palette) <- palette_df$color_names
# Define parameters for function
x_value <- PL_count_df$tumor_descriptor
title <- paste("Variant types in the paired longitudinal cohort", sep = " ")
# Run function
fname <- paste0(PL_plots_dir, "/", "Alteration_type_timepoints_barplots_PL.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/Alteration_type_timepoints_barplots_PL.pdf"
p <- create_stacked_barplot_variant(df = PL_count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
quartz_off_screen
2
# Define parameters for function
x_value <- PBTA_count_df$tumor_descriptor
title <- paste("Variant types in the PBTA cohort", sep = " ")
# Run function
fname <- paste0(PBTA_plots_dir, "/", "Alteration_type_timepoints_barplots_PBTA.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/Alteration_type_timepoints_barplots_PBTA.pdf"
p <- create_stacked_barplot_variant(df = PBTA_count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
quartz_off_screen
2
PL_panel_df <- PL_count_df %>%
mutate(cg_id = str_wrap(cg_id, 12)) # Edit to fit in the plot title for the panel
# Define parameters for function
x_value <- PL_panel_df$tumor_descriptor
title <- paste("Variant types across cancer groups in the paired longitudinal cohort", sep = " ")
rows <- 5
# Run function
fname <- paste0(PL_plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots_PL.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/Alteration_type_timepoints_cg_id_barplots_PL.pdf"
p <- create_stacked_barplot_variant_cg_id(df = PL_panel_df, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = 12, height = 15)
print(p)
dev.off()
quartz_off_screen
2
PBTA_panel_df <- PBTA_count_df %>%
mutate(cg_id = str_wrap(cg_id, 12)) # Edit to fit in the plot title for the panel
# Define parameters for function
x_value <- PBTA_panel_df$tumor_descriptor
title <- paste("Variant types across cancer groups in the PBTA cohort", sep = " ")
rows <- 10
# Run function
fname <- paste0(PBTA_plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots_PBTA.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/Alteration_type_timepoints_cg_id_barplots_PBTA.pdf"
p <- create_stacked_barplot_variant_cg_id(df = PBTA_panel_df, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = 15, height = 28)
print(p)
dev.off()
quartz_off_screen
2
PL_panel_df <- PL_count_df %>%
mutate(cg_id = str_replace_all(cg_id, " ", "_"),
# Edit to fit in the plot title for the panel
molecular_subtype = str_wrap(molecular_subtype, 12))
sample <- as.character(unique(PL_panel_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- PL_panel_df %>%
filter(cg_id == sample[i])
if (i %in% c(10, 16)){
width_value = 25
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$td_plot_group_n
title <- paste(sample[i], "Variants across molecular subtypes", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(molecular_subtype_PL_plots_dir, "/", sample[i], "_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf")
print(fname)
p <- create_stacked_barplot_variant_molecular_subtype(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Chordoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Diffuse_midline_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Ependymoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Ewing_sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Glial_neuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Hemangioblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/High_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Low_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Medulloblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Meningioma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/molecular_subtype_PL_plots/Schwannoma_Alteration_type_timepoints_molecular_subtype_barplots_PL.pdf"
PBTA_panel_df <- PBTA_count_df %>%
mutate(cg_id = str_replace_all(cg_id, " ", "_"),
molecular_subtype = str_wrap(molecular_subtype, 12)) # Edit to fit in the plot title for the panel
sample <- as.character(unique(PBTA_panel_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_choroid_plexus_papilloma"
[3] "Atypical_Teratoid_Rhabdoid_Tumor" "Cavernoma"
[5] "Central_neurocytoma" "Chondromyxoid_fibroma"
[7] "Chordoma" "Choroid_plexus_carcinoma"
[9] "Choroid_plexus_papilloma" "Choroid_plexus_tumor"
[11] "CNS_Burkitt's_lymphoma" "CNS_Embryonal_tumor"
[13] "CNS_neuroblastoma" "Craniopharyngioma"
[15] "Desmoplastic_infantile_astrocytoma_and_ganglioglioma" "Diffuse_fibrillary_astrocytoma"
[17] "Diffuse_hemispheric_glioma" "Diffuse_intrinsic_pontine_glioma"
[19] "Diffuse_leptomeningeal_glioneuronal_tumor" "Diffuse_midline_glioma"
[21] "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[23] "Ependymoma" "Epstein_Barr_virus-related_tumor"
[25] "Ewing_sarcoma" "Extraventricular_neurocytoma"
[27] "Ganglioglioma" "Ganglioneuroblastoma"
[29] "Ganglioneuroma" "Germinoma"
[31] "Glial_neuronal_tumor" "Hemangioblastoma"
[33] "High_grade_glioma" "Histiocytic_tumor"
[35] "Infant_type_hemispheric_glioma" "Inflammatory_Myofibroblastic_Tumor"
[37] "Langerhans_Cell_histiocytosis" "Low_grade_glioma"
[39] "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[41] "Melanocytic_tumor" "Meningioma"
[43] "Mesenchymal_tumor" "Metastatic_secondary_tumors"
[45] "Mixed_germ_cell_tumor" "Neuroblastoma"
[47] "Neurofibroma_Plexiform" "Non_germinomatous_germ_cell_tumor"
[49] "Oligodendroglioma" "Perineuroma"
[51] "Pilocytic_astrocytoma" "Pineoblastoma"
[53] "Pleomorphic_xanthoastrocytoma" "Rhabdomyosarcoma"
[55] "Rosai_Dorfman_disease" "Rosette_forming_glioneuronal_tumor"
[57] "Sarcoma" "Schwannoma"
[59] "Subependymal_Giant_Cell_Astrocytoma" "Teratoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- PBTA_panel_df %>%
filter(cg_id == sample[i])
if (i %in% c(25, 41)){
width_value = 25
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$td_plot_group_n
title <- paste(sample[i], "Variants across molecular subtypes", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(molecular_subtype_PBTA_plots_dir, "/", sample[i], "_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf")
print(fname)
p <- create_stacked_barplot_variant_molecular_subtype(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Atypical_choroid_plexus_papilloma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Cavernoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Central_neurocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Chondromyxoid_fibroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Chordoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_papilloma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_Burkitt's_lymphoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Desmoplastic_infantile_astrocytoma_and_ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_fibrillary_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_hemispheric_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_intrinsic_pontine_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_leptomeningeal_glioneuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_midline_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ependymoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 24
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Epstein_Barr_virus-related_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 25
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ewing_sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 26
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Extraventricular_neurocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 27
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 28
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioneuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 29
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioneuroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 30
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Germinoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 31
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Glial_neuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 32
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Hemangioblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 33
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/High_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 34
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Histiocytic_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 35
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Infant_type_hemispheric_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 36
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Inflammatory_Myofibroblastic_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 37
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Langerhans_Cell_histiocytosis_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 38
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Low_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 39
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 40
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Medulloblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 41
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Melanocytic_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 42
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Meningioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 43
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Mesenchymal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 44
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Metastatic_secondary_tumors_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 45
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Mixed_germ_cell_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 46
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 47
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 48
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Non_germinomatous_germ_cell_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 49
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Oligodendroglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 50
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Perineuroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 51
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 52
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pineoblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 53
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pleomorphic_xanthoastrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 54
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rhabdomyosarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 55
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rosai_Dorfman_disease_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 56
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rosette_forming_glioneuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 57
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 58
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Schwannoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 59
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Subependymal_Giant_Cell_Astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 60
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Teratoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
cg_df <- PL_count_df %>%
# Fix syntax in cancer groups names
mutate(cg_id = str_replace_all(cg_id, " ", "_"))
sample <- as.character(unique(cg_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- cg_df %>%
filter(cg_id == sample[i]) %>%
mutate(tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order_abbrev),
Variant_Classification = factor(Variant_Classification),
Variant_Classification = fct_relevel(Variant_Classification, variants_order)) %>%
arrange(tumor_descriptor, Variant_Classification)
if (i %in% c(2, 7, 15, 18)){
width_value = 25
}else if (i %in% c(10, 16)){
width_value = 36
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$td_ms_plot_group
title <- paste(sample[i], "Variants across samples", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(kids_molecular_subtype_PL_plots_dir, "/", sample[i], "_Alteration_type_timepoints_kids_barplots_PL.pdf")
print(fname)
p <- create_stacked_barplot_variant_kids(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
Warning: There were 42 warnings in `mutate()`.
The first warning was:
ℹ In argument: `tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order_abbrev)`.
ℹ In group 1: `tumor_descriptor = Diagnosis`, `td_ms_plot_group = "Dx:ADAM"`, `cg_id = "Adamantinomatous_Craniopharyngioma"`, `molecular_subtype =
"CRANIO ADAM"`, `Kids_First_Participant_ID = "PT_CBTW4E3X"`, `match_id = "Diagnosis_PT_CBTW4E3X"`, `Variant_Classification = Missense_Mutation`,
`td_ms_plot_group_n = "Dx:ADAM (N=27)"`, `td_plot_group_n = "Diagnosis (N=27)"`.
Caused by warning:
! 8 unknown levels in `f`: Dx, Pro, Rec, Dec, SM, Unavail, Metastatic, and Residual
ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 41 remaining warnings.
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Chordoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Diffuse_midline_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Ependymoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Ewing_sarcoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Ganglioglioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Glial_neuronal_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Hemangioblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/High_grade_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Low_grade_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Medulloblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Meningioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Neuroblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_molecular_subtype_PL_plots/Schwannoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
cg_df <- PL_count_df %>%
# Fix syntax in cancer groups names
mutate(cg_id = str_replace_all(cg_id, " ", "_"))
sample <- as.character(unique(cg_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- cg_df %>%
filter(cg_id == sample[i])
if (i %in% c(2, 7, 15, 18)){
width_value = 25
}else if (i %in% c(10, 16)){
width_value = 28
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$td_ms_plot_group_n
title <- paste(sample[i], "Variants across samples", sep = ": ")
rows <- 1
# Run function
fname <- paste0(kids_PL_plots_dir, "/", sample[i], "_Alteration_type_timepoints_kids_barplots_PL.pdf")
print(fname)
p <- create_stacked_barplot_variant_kids(df = df_sub, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Chordoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Diffuse_midline_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Ependymoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Ewing_sarcoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Ganglioglioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Glial_neuronal_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Hemangioblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/High_grade_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Low_grade_glioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Medulloblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Meningioma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Neuroblastoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PL/kids_PL_plots/Schwannoma_Alteration_type_timepoints_kids_barplots_PL.pdf"
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggthemes_4.2.4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.3 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[10] ggplot2_3.4.4 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] sass_0.4.7 utf8_1.2.4 generics_0.1.3 stringi_1.7.12 hms_1.1.3 digest_0.6.33 magrittr_2.0.3 evaluate_0.23
[9] timechange_0.2.0 fastmap_1.1.1 rprojroot_2.0.4 jsonlite_1.8.7 fansi_1.0.5 scales_1.2.1 jquerylib_0.1.4 cli_3.6.1
[17] rlang_1.1.2 crayon_1.5.2 bit64_4.0.5 munsell_0.5.0 cachem_1.0.8 withr_2.5.2 yaml_2.3.7 tools_4.3.1
[25] parallel_4.3.1 tzdb_0.4.0 colorspace_2.1-0 vctrs_0.6.4 R6_2.5.1 lifecycle_1.0.4 bit_4.0.5 vroom_1.6.4
[33] pkgconfig_2.0.3 pillar_1.9.0 bslib_0.5.1 gtable_0.3.4 glue_1.6.2 xfun_0.41 tidyselect_1.2.0 rstudioapi_0.15.0
[41] knitr_1.45 farver_2.1.1 htmltools_0.5.7 rmarkdown_2.25 labeling_0.4.3 compiler_4.3.1